data_HYP
#
_chem_comp.id HYP
_chem_comp.name 4-HYDROXYPROLINE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C5 H9 N O3'
_chem_comp.mon_nstd_parent_comp_id PRO
_chem_comp.pdbx_synonyms HYDROXYPROLINE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-09-27
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 131.130
_chem_comp.one_letter_code P
_chem_comp.three_letter_code HYP
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
_chem_comp.pdbx_pcm Y
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
HYP N N N 0 1 N N N Y Y N -3.366 16.585 44.188 0.168 1.360 -0.282 N HYP 1
HYP CA CA C 0 1 N N S Y N N -2.955 15.768 43.044 -0.384 -0.003 -0.493 CA HYP 2
HYP C C C 0 1 N N N Y N Y -1.447 15.609 43.030 -1.811 -0.072 -0.013 C HYP 3
HYP O O O 0 1 N N N Y N Y -0.722 16.484 43.503 -2.233 0.764 0.750 O HYP 4
HYP CB CB C 0 1 N N N N N N -3.408 16.578 41.829 0.515 -0.924 0.359 CB HYP 5
HYP CG CG C 0 1 N N R N N N -4.437 17.482 42.330 1.847 -0.159 0.505 CG HYP 6
HYP CD CD C 0 1 N N N N N N -4.068 17.803 43.753 1.640 1.159 -0.271 CD HYP 7
HYP OD1 OD O 0 1 N N N N N N -5.693 16.815 42.294 2.917 -0.911 -0.071 OD1 HYP 8
HYP OXT OXT O 0 1 N Y N Y N Y -0.976 14.502 42.469 -2.614 -1.063 -0.433 OXT HYP 9
HYP H H H 0 1 N Y N Y Y N -3.980 16.047 44.765 -0.107 1.981 -1.028 H HYP 10
HYP HA HA H 0 1 N N N Y N N -3.385 14.756 43.068 -0.325 -0.278 -1.546 HA HYP 11
HYP HB2 1HB H 0 1 N N N N N N -2.567 17.141 41.398 0.066 -1.092 1.337 HB2 HYP 12
HYP HB3 2HB H 0 1 N N N N N N -3.790 15.930 41.026 0.678 -1.873 -0.153 HB3 HYP 13
HYP HG HG H 0 1 N N N N N N -4.508 18.399 41.726 2.052 0.048 1.555 HG HYP 14
HYP HD22 1HD H 0 0 N N N N N N -4.956 18.005 44.370 2.018 1.065 -1.289 HD22 HYP 15
HYP HD23 2HD H 0 0 N N N N N N -3.457 18.713 43.848 2.132 1.985 0.243 HD23 HYP 16
HYP HD1 HOD H 0 1 N N N N N N -5.999 16.666 43.181 3.780 -0.479 -0.009 HD1 HYP 17
HYP HXT HXT H 0 1 N Y N Y N Y -0.027 14.511 42.499 -3.520 -1.066 -0.098 HXT HYP 18
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
HYP N CA SING N N 1
HYP N CD SING N N 2
HYP N H SING N N 3
HYP CA C SING N N 4
HYP CA CB SING N N 5
HYP CA HA SING N N 6
HYP C O DOUB N N 7
HYP C OXT SING N N 8
HYP CB CG SING N N 9
HYP CB HB2 SING N N 10
HYP CB HB3 SING N N 11
HYP CG CD SING N N 12
HYP CG OD1 SING N N 13
HYP CG HG SING N N 14
HYP CD HD22 SING N N 15
HYP CD HD23 SING N N 16
HYP OD1 HD1 SING N N 17
HYP OXT HXT SING N N 18
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
HYP SMILES ACDLabs 10.04 'O=C(O)C1NCC(O)C1'
HYP SMILES_CANONICAL CACTVS 3.341 'O[C@H]1CN[C@@H](C1)C(O)=O'
HYP SMILES CACTVS 3.341 'O[CH]1CN[CH](C1)C(O)=O'
HYP SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C1[C@H](CN[C@@H]1C(=O)O)O'
HYP SMILES 'OpenEye OEToolkits' 1.5.0 'C1C(CNC1C(=O)O)O'
HYP InChI InChI 1.03 'InChI=1S/C5H9NO3/c7-3-1-4(5(8)9)6-2-3/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4+/m1/s1'
HYP InChIKey InChI 1.03 PMMYEEVYMWASQN-DMTCNVIQSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
HYP 'SYSTEMATIC NAME' ACDLabs 10.04 '(4R)-4-hydroxy-L-proline'
HYP 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S,4R)-4-hydroxypyrrolidine-2-carboxylic acid'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HYP 'Create component' 1999-07-08 PDBJ
HYP 'Modify descriptor' 2011-06-04 RCSB
HYP 'Modify synonyms' 2021-03-01 PDBE
HYP 'Modify backbone' 2023-11-03 PDBE
HYP 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id HYP
_pdbx_chem_comp_synonyms.name HYDROXYPROLINE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id HYP
_pdbx_chem_comp_pcm.modified_residue_id PRO
_pdbx_chem_comp_pcm.type Hydroxylation
_pdbx_chem_comp_pcm.category 'Named protein modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession PTM-0043
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession PTM-0149
#
_pdbe_chem_comp_drugbank_details.comp_id HYP
_pdbe_chem_comp_drugbank_details.drugbank_id DB08847
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Hydroxyproline
_pdbe_chem_comp_drugbank_details.description
'Hydroxyproline is a neutral heterocyclic protein amino acid. It is found in collagen and as such it is common in many gelatin products. Hydroxyproline is mostly used as a diagnostic marker of bone turnover and liver fibrosis. Therapeutically, hydroxyproline is being studied as an an experimental medicine but is approved in France as a combination topical gel product called Cicactive for small, superficial wounds.'
_pdbe_chem_comp_drugbank_details.cas_number 51-35-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
HYP HYDROXYPROLINE wwPDB ?
HYP trans-4-Hydroxy-L-proline DrugBank ?
HYP trans-L-Hydroxyproline DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id HYP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB08847
_pdbe_chem_comp_drugbank_classification.parent 'Proline and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as proline and derivatives. These are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.'
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
HYP N N 7.639 -1.236 1
HYP CA C 6.426 -0.355 2
HYP C C 4.999 -0.818 3
HYP O O 3.884 0.185 4
HYP CB C 6.889 1.072 5
HYP CG C 8.389 1.072 6
HYP CD C 8.853 -0.355 7
HYP OD1 O 9.271 2.285 8
HYP OXT O 4.687 -2.285 9
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
HYP N CA SINGLE NONE 1
HYP N CD SINGLE NONE 2
HYP CA C SINGLE BEGINDASH 3
HYP CA CB SINGLE NONE 4
HYP C O DOUBLE NONE 5
HYP C OXT SINGLE NONE 6
HYP CB CG SINGLE NONE 7
HYP CG CD SINGLE NONE 8
HYP CG OD1 SINGLE BEGINWEDGE 9
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
HYP MurckoScaffold S1 scaffold C1CCNC1 InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2 RWRDLPDLKQPQOW-UHFFFAOYSA-N
HYP peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
HYP N S1 1
HYP CA S1 1
HYP CB S1 1
HYP CG S1 1
HYP CD S1 1
HYP O F1 1
HYP C F1 1
HYP CA F1 1
HYP N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HYP
_pdbe_chem_comp_rdkit_properties.exactmw 131.058
_pdbe_chem_comp_rdkit_properties.amw 131.131
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 65.369
_pdbe_chem_comp_rdkit_properties.tpsa 69.560
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.206
_pdbe_chem_comp_rdkit_properties.CrippenMR 30.050
_pdbe_chem_comp_rdkit_properties.chi0v 4.172
_pdbe_chem_comp_rdkit_properties.chi1v 2.060
_pdbe_chem_comp_rdkit_properties.chi2v 0.695
_pdbe_chem_comp_rdkit_properties.chi3v 0.695
_pdbe_chem_comp_rdkit_properties.chi4v 0.367
_pdbe_chem_comp_rdkit_properties.chi0n 13.172
_pdbe_chem_comp_rdkit_properties.chi1n 6.323
_pdbe_chem_comp_rdkit_properties.chi2n 0.695
_pdbe_chem_comp_rdkit_properties.chi3n 0.695
_pdbe_chem_comp_rdkit_properties.chi4n 0.367
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.610
_pdbe_chem_comp_rdkit_properties.kappa1 1.515
_pdbe_chem_comp_rdkit_properties.kappa2 2.326
_pdbe_chem_comp_rdkit_properties.kappa3 1.399
_pdbe_chem_comp_rdkit_properties.Phi 0.392
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
HYP UniChem ChEMBL CHEMBL352418
HYP UniChem DrugBank DB08847
HYP UniChem 'Guide to Pharmacology' 4704
HYP UniChem 'KEGG LIGAND' C01157
HYP UniChem ChEBI 18095
HYP UniChem ChEBI 58375
HYP UniChem ZINC ZINC000000901791
HYP UniChem eMolecules 521697
HYP UniChem fdasrs RMB44WO89X
HYP UniChem SureChEMBL SCHEMBL21185
HYP UniChem HMDB HMDB0000725
HYP UniChem PubChem 5810
HYP UniChem PubChem 6971053
HYP UniChem NMRShiftDB 60020634
HYP UniChem Recon '4hpro_LT'
HYP UniChem Nikkaji J148.015D
HYP UniChem BindingDb 50357233
HYP UniChem 'EPA CompTox Dashboard' DTXSID10883225
HYP UniChem DrugCentral 4272
HYP UniChem MetaboLights MTBLC18095
HYP UniChem MetaboLights MTBLC58375
HYP UniChem BRENDA 12713
HYP UniChem BRENDA 221345
HYP UniChem BRENDA 228695
HYP UniChem BRENDA 36576
HYP UniChem BRENDA 6646
HYP UniChem Rhea 58375
HYP UniChem ChemicalBook CB8357870
HYP UniChem rxnorm HYDROXYPROLINE
HYP UniChem MedChemExpress HY-40135
HYP UniChem 'Probes And Drugs' PD051320
HYP UniChem CCDC HOPROL
HYP UniChem 'PubChem TPHARMA' 15218989
HYP UniChem 'PubChem TPHARMA' 16783819
HYP UniChem Mcule MCULE-5389747201
HYP UniChem Mcule MCULE-6465399562
HYP UniChem ACTor 147028-80-6
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
HYP N 0.100 -1.053 0.725 ETKDGv3 1
HYP CA 0.637 -0.263 -0.386 ETKDGv3 2
HYP C 2.112 0.008 -0.229 ETKDGv3 3
HYP O 2.653 0.952 -0.868 ETKDGv3 4
HYP CB -0.196 1.011 -0.457 ETKDGv3 5
HYP CG -1.562 0.587 0.067 ETKDGv3 6
HYP CD -1.336 -0.771 0.743 ETKDGv3 7
HYP OD1 -2.512 0.499 -0.967 ETKDGv3 8
HYP OXT 2.899 -0.829 0.557 ETKDGv3 9
HYP H 0.495 -0.683 1.624 ETKDGv3 10
HYP HA 0.496 -0.840 -1.327 ETKDGv3 11
HYP HB2 0.228 1.791 0.215 ETKDGv3 12
HYP HB3 -0.241 1.409 -1.495 ETKDGv3 13
HYP HG -1.922 1.328 0.815 ETKDGv3 14
HYP HD22 -1.721 -0.757 1.788 ETKDGv3 15
HYP HD23 -1.867 -1.583 0.199 ETKDGv3 16
HYP HD1 -2.161 -0.131 -1.651 ETKDGv3 17
HYP HXT 3.895 -0.672 0.648 ETKDGv3 18
#